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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('epigenomix_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing epigenomix ───────────────────────────────────────────────────────
✔ Package installed successfully
── epigenomix session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpyFPQUh/file88457557f204e/epigenomix
→ BiocVersion: 3.24
→ Package: epigenomix
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/epigenomix.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpyFPQUh/file88457557f204e/epigenomix
→ installDir: /tmp/RtmpyFPQUh/file884572de85c8a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on epigenomix ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Transcription,
Sequencing, Coverage, Normalization, KEGG, Preprocessing, Bayesian
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (75%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • epigenomix.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • epigenomix.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • epigenomix.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/epigenomix.Rnw
* Checking package installation calls in R code...
* Checking for library/require of epigenomix...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/calculateCrossCorrelation.R (line 20, column 15)
    • ...
    • R/summarizeReads.R (line 36, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • bayesMixModel.R (line 92, column 15)
    • ...
    • summarizeReads.R (line 20, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bayesMixModel.R (line 230, column 11)
    • ...
    • R/plotComponents.R (line 19, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/calculateCrossCorrelation.R (line 11, column 15)
    • ...
    • R/plotChains.R (line 119, column 17)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • integrateData.R (line 8, column 36)
    • integrateData.R (line 8, column 84)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/normalizeChIP.R (line 3, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/matchProbeToPromoter.R (line 73, column 24)
  • suppressWarnings() in R/matchProbeToPromoter.R (line 74, column 15)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • .bayesMixModel() (R/bayesMixModel.R): 432 lines
    • ...
    • .mlMixModel() (R/mlMixModel.R): 108 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotChains.Rd
    • man/plotClassification.Rd
    • man/plotComponents.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getAlignmentQuality.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • getAlignmentQuality.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • getAlignmentQuality.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 308 lines (7%) are > 80 characters long.
  First few lines:
    • R/AllGenerics.R#L3 colDat ...
    • ...
    • vignettes/epigenomix.Rnw#L246 This is in line with the fact that H3K4m
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 6 lines (0%) contain tabs.
  First few lines:
    • R/methods-ChIPseqSet.R#L50 priorCountScaled <- libSize / mean(libS ...
    • ...
    • man/MixModel-class.Rd#L56 "MixModel")}: List available classifica ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1487 lines (36%) are
not.
  First few lines:
    • R/AllClasses.R#L2 contains = "RangedSummarizedExp ...
    • ...
    • vignettes/epigenomix.Rnw#L244 classification(bayesmm, method="mo ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 21 NOTES
ℹ See the epigenomix.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.